Cell-type specific sequencing of microRNAs from complex animal tissues

Alberti, Chiara; Manzenreither, Raphael A.; Sowemimo, Ivica; Burkard, Thomas R; Wang, Jingkui; Mahofsky, Katharina; Ameres, Stefan L.; Cochella, Luisa

doi:10.1038/nmeth.4610

Cited by 77 publications

(112 citation statements)

References 69 publications

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“…Further cell-type-specific sequencing of miRNAs (Alberti et al, 2018) will allow the design of mAGNETs to target a greater repertoire of neuron types across more species. In addition to targeting known cell types, mAGNETs could also be useful for defining new neuron subtypes.…”

Section: Discussionmentioning

confidence: 99%

A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex

Keaveney

Tseng

et al. 2018

Cell Reports

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In Brief Viral targeting of neuron subtypes is desirable for neuroscience research. Keaveney et al. developed a microRNA-based viral tool for labeling cortical interneurons. They demonstrate its utility via neuron subtype labeling in a murine disease model and in rats and through dual-color optogenetic control of two neuron types. SUMMARY More specific and broadly applicable viral gene-targeting tools for labeling neuron subtypes are needed to advance neuroscience research, especially in rodent transgenic disease models and genetically intractable species. Here, we develop a viral vector that restricts transgene expression to GABAergic interneurons in the rodent neocortex by exploiting endogenous microRNA regulation. Our interneurontargeting, microRNA-guided neuron tag, ‘‘GABA mAGNET,’’ achieves >95% interneuron selective labeling in the mouse cortex, including in a murine model of autism and also some preferential labeling of interneurons in the rat brain. We demonstrate an application of our GABA mAGNET by performing simultaneous, in vivo optogenetic control of two distinct neuron subtypes. This interneuron labeling tool highlights the potential of microRNA-based viral gene targeting to specific neuron subtypes.

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Section: Discussionmentioning

confidence: 99%

A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex

Keaveney

Tseng

et al. 2018

Cell Reports

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“…Understanding endogenous miRNA functions precisely requires approaches to profile miRNAs and their targets simultaneous in single cell resolution. Though some approaches that enables high-throughput sequencing of single cell miRNAs were proposed very recently [49,50], the paired high quality data of miRNA and their target in the same single cell are still lacking, which prevents for the discovery of associations between transcriptional and miRNA profile variation. These questions may be further addressed by multi-omics profiling of single cells in the future.…”

Section: Discussionmentioning

confidence: 99%

Single cell transcriptomes reveal characteristics of miRNA in gene expression noise reduction

Wei

et al. 2018

Preprint

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Isogenic cells growing in identical environments show cell-to-cell variations becauseof stochastic gene expression. The high level of variation or noise could disrupt robust gene expression and result in tremendous consequences on cell behaviors. In this work, we showed evidence that microRNAs (miRNAs) could reduce gene expression noise in mRNA level of mouse cells based on single-cell RNA-sequencing data analysis. We identified that miRNA expression level, number of targets, targets pool abundance and interaction strength of miRNA with its targets are the key features contributing to noise repression. MiRNAs tend to work together as cooperative sub-networks to repress target noise synergistically in a cell type specific manner. Using a physical model of post-transcriptional regulation, we demonstrated that the accelerated degradation with elevated transcriptional activation of miRNA target provides resistance to extrinsic fluctuations. Together, through the integration analysis of single-cell RNA and miRNA expression profiles. We demonstrated that miRNAs are important post-transcriptional 2 regulators for reducing gene expression noise and conferring robustness to biological processes.

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“…In addition, environmentally induced transcriptional reprogramming is evident following labelling (Figure 4h-k). As opposed to recently described methods [14, 17, 20, 22] and in keeping with the literature where POLI, POLII and POLIII are demonstrated to incorporate 5EU [27], mRNA and small RNAs of various types including rRNA, tRNA and miRNA are found to be labeled and enriched in pulled-down RNA.…”

Section: Discussionmentioning

confidence: 55%

“…Both TU and EC tagging use cre-recombination to express the relevant enzymes in a tissue specific manner and stochastic expression from the cre-promoter may lead to unwanted expression of the enzymes in different tissues [21]. Finally, one recently developed method called Mime-seq allows for cell type specific labeling of microRNA [22]. In this method, tissue specific expression of a plant derived methyltransferase mediates a 3′-terminal 2′-O-methylation of microRNAs that, when combined with a methylation dependent library construction, allows for sequencing of tissue specific microRNAs.…”

Section: Introductionmentioning

confidence: 99%

In-vivo targeted tagging of RNA isolates cell specific transcriptional responses to environmental stimuli and identifies liver-to-adipose RNA transfer

Darr

Lassi

Tomar

et al. 2019

Preprint

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19Bio-fluids contain various circulating cell-free RNA transcripts (ccfRNAs). The composition of 20 these ccfRNAs varies between bio-fluids and constitute tantalizing biomarker candidates for 21 several pathologies. ccfRNAs have also been demonstrated as mediators of cellular 22 communication, yet little is known about their function in physiological and developmental 23 settings and most works are limited to in-vitro studies. Here, we have developed iTAG-RNA, a 24 novel method for the unbiased tagging of RNA transcripts in mice in-vivo. We used this method 25 to isolate hepatocytes and kidney proximal epithelial cells-specific transcriptional response to a 26 dietary challenge without interfering with the tissue architecture, and to identify multiple 27 hepatocyte-secreted ccfRNAs in plasma. We also identified transfer of these hepatic derived 28 ccfRNAs to adipose tissue, where they likely serve as a buffering mechanism to maintain 29 cholesterol and lipid homeostasis. Our findings directly demonstrate in-vivo transfer of RNAs 30 between tissues and highlight its implications for endocrine signaling and homeostasis.Little is known about the biological function of circulating cell-free RNAs (ccfRNA). Found to be 34 associated with exosomes, lipoproteins, ribonucleoproteins and more, these transcripts can be 35 isolated and sequenced from multiple bio-fluids such as plasma, lymph, cerebral fluids, breast milk 36 and more [1, 2]. ccfRNAs are directly implicated in the development of several pathologies 37 including cancer and obesity [3][4][5] and are intensively studied as disease biomarkers [6, 7]. Despite 38 this, the role they play in physiological and developmental settings and in mediating cell-to-cell 39 communication remains largely unknown. In-vitro, a growing number of works demonstrate the 40 relevance of RNA based cellular communication [8][9][10][11], however in-vivo evidence is still limited. 41This discrepancy is partly due to the difficulties posed to tracking ccfRNAs from transcriptional 42 source to potential sites of action in-vivo. Indeed the tools available to study ccfRNAs in 43 physiological settings are limited and very few studies attempt to tackle this problem directly. 44One work found evidence to suggest that the majority of circulating miRNAs originate in adipose 45 tissue and that some of the adipose derived miRNAs may play a role in the regulation of liver 46 Fgf21 levels [12]. However, this work focuses on miRNA and does not directly demonstrate 47 transfer of RNAs between tissues nor directly identify adipose secreted RNAs. 48Transfer of miRNAs was also demonstrated between epithelial cells of the caput epididymis to 49 maturing spermatozoa, leading to a shift in sperm RNA content during its maturation [13]. This 50 study made use of 4-thiouracil-tagging (TU-tagging) [14] combined with SLAM-Seq [15] to 51 demonstrate loading of miRNAs transcribed in caput epididymis into maturing spermatozoa. TU-52 tagging entails cell-type specific expression of uracil phosphoribosyltransferase...

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Cell-type specific sequencing of microRNAs from complex animal tissues

Cited by 77 publications

References 69 publications

A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex

A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex

Single cell transcriptomes reveal characteristics of miRNA in gene expression noise reduction

In-vivo targeted tagging of RNA isolates cell specific transcriptional responses to environmental stimuli and identifies liver-to-adipose RNA transfer

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